Use Grinders, Mechanical Presses and Mechanical Mixers to process items into different, likely more useful or compact items, transport them with lines of Conveyors and sort them out with Item Splitters and Funnels into their own respective Wooden Containers. Just remember to create a Windmill or Steam Engine, as using Hand Crank for everything isn’t ideal. Then, if you think you are done with machinery, you can use some Item Readers, Item Counters connected to Nixie Tubes via colored Cables to display information in a nice and visible way!
Official Wiki: https://modded.wiki/w/Mod:PolyFactory